Identifying the species diversity of an ecosystem provides valuable insights into the impact of environmental changes, as well as ecosystem recovery. A large proportion of petrels and prions are listed as threatened; however, these species are often cryptic breeders and difficult to study. This case study assessed the value of incorporating DNA methods into field surveys to identify burrowing petrel species and distribution by using scats and feather samples collected near burrows as part of a monitoring program on Macquarie Island.